User: Sara

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Sara60
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2 months, 2 weeks ago
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1 year, 9 months ago
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Posts by Sara

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Differential gene expression analysis vs disease-gene expression association
... So many thanks kevin! ...
written 11 weeks ago by Sara60
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Comment: C: Differential gene expression analysis vs disease-gene expression association
... Thanks Kevin, but if you check the methods they used the same approach for both analysis. Indeed, they did not use any common approach of differential expression analysis like Deseq2 and they did association analysis. So, my main question is, did they misuse the "differential gene expression" phrase ...
written 11 weeks ago by Sara60
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Comment: C: Differential gene expression analysis vs disease-gene expression association
... Hi Kevin, for example in [this paper][1] they used gene-expression association analysis using a regression model. It was confusing for me that they named the associated genes as the differentially expressed genes while differential gene expression analysis has its own methods and packages like Deseq ...
written 11 weeks ago by Sara60
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Differential gene expression analysis vs disease-gene expression association
... Hi All! Can anybody help me to understand what is the difference between differential gene expression analysis vs disease-gene expression association analysis? Any help is appreciated! ...
rna-seq differential gene expression analysis written 11 weeks ago by Sara60
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Comment: C: FPKM quantile normalization
... Do you mean for example log transformation? ...
written 19 months ago by Sara60
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Comment: C: FPKM quantile normalization
... Yes, when I did not receive any reply from you, because I was in a hurry to do my project, I asked my question in Bioconductor support. Ok, I will link both question to each other. Thanks. ...
written 19 months ago by Sara60
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Comment: C: FPKM quantile normalization
... Many thanks Kevin. I downloaded the genecode version 19 gtf file and put it in my document. I am so thankful for your valuable advice to use Deseq2 normalization with gene adjustment. ...
written 19 months ago by Sara60
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Comment: C: FPKM quantile normalization
... I finally found the way to do this. Here is the R code for whoever needs it. cts <- as.matrix(read.csv("Count_data.txt", row.names = 1, header= TRUE, sep="\t")) coldata <- read.csv("coldata.txt", row.names = 1, sep="\t") dds <- DESeqDataSetFromMatrix(countData = cts, colData = ...
written 19 months ago by Sara60
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Comment: C: FPKM quantile normalization
... Many thanks Kevin, I have a look at [tximport][1], but I confused. How can i do that? I have gene-level counts, not transcripts level. [1]: http://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html ...
written 19 months ago by Sara60
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Comment: C: FPKM quantile normalization
... For example see this paper : https://www.pnas.org/content/115/50/E11874.short At the supplementary data, FPKM quantile normalization has been explained. ...
written 19 months ago by Sara60

Latest awards to Sara

Popular Question 18 months ago, created a question with more than 1,000 views. For FPKM quantile normalization
Student 18 months ago, asked a question with at least 3 up-votes. For Which normalization is good for gene expression classification and clustering

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